Performs one iteration of the single component adaptative Metropolis (SCAM) algorithm with eigenvector rotation. scamH
is designed to apply the SCAM algorithm for models where a species community is modelled using habitat characteristics whereas scamHT
applies the SCAM algorithm to model a community with habitat characteristics and species traits.
1 2 3 4 5 6 7 8 9 10 11  ## S3 method for class 'formula'
scamH(formula,data,start,priors,rotationVal,rotationVect,wParamX,wOuterParamX,sdvalue,accept,likelihoodtype="logit",burning=TRUE,rotation=TRUE,iter,...)
## S3 method for class 'HMSCdata'
scamH(data,start,priors,rotationVal,rotationVect,wParamX,wOuterParamX,sdvalue,accept,likelihoodtype="logit",burning=TRUE,rotation=TRUE,iter,...)
## S3 method for class 'HMSCdata'
scamHT(data,start,priors,rotationVal,rotationVect,wParamX,wOuterParamX,sdvalue,accept,likelihoodtype="logit",burning=TRUE,rotation=TRUE,iter,...)
## S3 method for class 'HMSCdata'
scamRandom(data,start,priors,rotationVal,rotationVect,wParamRandom,wOuterParamRandom,wRandomCov,sdvalue,accept,likelihoodtype="logit",burning=TRUE,rotation=TRUE,iter,...)

formula 
Model formula. The left side presents the response matrix and the right side gives the descriptors with their parameters. (See details) 
data 
Object of class HMSCdata. 
start 
Object of class HMSCparam. 
priors 
Object of class HMSCprior. 
rotationVal 
Matrix of eigenvalues independently weighting the importance of each parameter for a response variables. The matrix has as many rows as there are response variables and as many columns as parameters. 
rotationVect 
3dimensional array where the first two dimensions present eigenvectors (indexed as the second dimension) for each response variables (third dimension). 
wParamX 
Matrix of the same dimensions as 
wOuterParamX 
3dimensional array presenting covariance matrices (the first two dimensions are the rows and columns of the covariance matrix and the third dimension presents the different covariance matrices) used to weight the importance of the parameters for each response variable. 
wParamRandom 
Matrix of the same dimensions as 
wOuterParamRandom 
3dimensional array presenting covariance matrices (the first two dimensions are the rows and columns of the covariance matrix and the third dimension presents the different covariance matrices) used to weight the importance of the random effect parameters for each response variable. 
wRandomCov 
A scalar weighting of the importance of 
sdvalue 
For 
accept 
For 
likelihoodtype 
Character string defining how the likelihood should be calculated. Any unambiguous variation of wording used in this argument is accepted. (See details) 
burning 
Logical. Whether or not standard deviation should be adapted. 
rotation 
Logical. Whether or not an eigenvector rotation should be carried out. 
iter 
Numeric. The number of time 
... 
Parameters passed to other functions. 
For the user the main difference between scamH
and scamHT
is within the data
and start
arguments. As for scamRandom
, it is specifically designed to estimate the parameter of the random effect and it is specifically it is heavily relying on the data and parameters available in the data
and start
arguments.
The algorithm implemented in this function assumes that the data follows a multivariate normal distribution. In that instance, it becomes valuable to check the distribution of the posterior to make sure that it is distributed following a pattern that look somewhat like a multivariate normal distribution. A way to do this is to use pairs
to study the different models parameters (paramX, paramTr,paramRandom, means, sigma,...), see example in hmscH
.
The formula
was designed so that it is necessary to include the parameters and the descriptors. This function is thus capable of carrying out nonlinear regression analyses. *** IMPORTANT : Although the function will run, the estimation of the parameters for a nonlinear model is very difficult and it is unlikely to converge unless many, many (many !!) iterations are carried out.***
Currently, two likelihood have been implemented, the binomial likelihood with a logit link, and the Poisson likelihood.
These functions were designed to converge to an accept ratio of 0.44.
These functions are constructed in such a way that if burning
is set to FALSE
, by default, rotation
will be considered FALSE
as well.
These functions are meant to be used within other functions such as hmscH
. However, this help file was written for user who want to develop new approaches using this basic algorithm.
start 
Object of class 
rotation 
List with the following items:

For scamH
and scamHT
:

An object of the same dimension as the argument 

An object of the same dimension as the argument 
For scamRandom
:
sdvalue 
A list of three component containing the updated standard deviations. This list includes exactly the same components as the ones first included in the function as argument. 
accept 
A list of three component containing the updated standard deviations. This list includes exactly the same components as the ones first included in the function as argument. 
No example are given for this function because this function is meant to be ran within another function. As explained in the Details section above.
F. Guillaume Blanchet
hmscH
, hmscHT
, loglikelihood
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
All documentation is copyright its authors; we didn't write any of that.